* using log directory 'd:/Rcompile/CRANpkg/local/4.7/ulrb.Rcheck' * using R Under development (unstable) (2026-07-09 r90225 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.3.0 GNU Fortran (GCC) 14.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * current time: 2026-07-10 21:31:29 UTC * checking for file 'ulrb/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ulrb' version '0.1.8' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'ulrb' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [1s] OK * checking whether the package can be loaded with stated dependencies ... [1s] OK * checking whether the package can be unloaded cleanly ... [1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s] OK * checking whether the namespace can be unloaded cleanly ... [1s] OK * checking loading without being on the library search path ... [1s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [4s] OK * checking Rd files ... [1s] OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... [1s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [10s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [124s] ERROR Running 'testthat.R' [124s] Running the tests in 'tests/testthat.R' failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(ulrb) > > test_check("ulrb") Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` If half the observations within a classification are below 0.5 Silhouette score, we consider that the clustering was 'Bad'. Check 'Evaluation' collumn for more details. Joining with `by = join_by(Sample, Level)` If half the observations within a classification are below 0.5 Silhouette score, we consider that the clustering was 'Bad'. Check 'Evaluation' collumn for more details. Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Automatic option set to TRUE, so classification vector was overwritten K= 2 based on Average Silhouette Score. Joining with `by = join_by(Sample, Level)` Automatic option set to TRUE, so classification vector was overwritten K= 9 based on Calinski-Harabasz. Joining with `by = join_by(Sample, Level)` Automatic option set to TRUE, so classification vector was overwritten K= 9 based on Calinski-Harabasz. Joining with `by = join_by(Sample, Level)` Automatic option set to TRUE, so classification vector was overwritten K= 5 based on Average Silhouette Score. Joining with `by = join_by(Sample, Level)` Automatic option set to TRUE, so classification vector was overwritten Joining with `by = join_by(Sample, Level)` Saving _problems/test-define_rb-264.R Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Ignoring unknown labels: * fill : "" Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Joining with `by = join_by(Sample, Level)` Missing argument sample_names. This is a vector with the names of the samples, as in the data input Taxa_id assumes each column is a taxonomic unit. Taxa_id assumes each column is a taxonomic unit. [ FAIL 1 | WARN 235 | SKIP 0 | PASS 153 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-define_rb.R:263:3'): No warning, if there are no clusters with zero taxa ── Expected `define_rb(no_singles, check_singles = TRUE)` not to throw any warnings. Actually got a with message: There were 4 warnings in `mutate()`. The first warning was: i In argument: `pam_object = purrr::map(...)`. i In group 1: `Sample = "ERR2044665"`. Caused by warning in `structure()`: ! Replacing special names '.Names' is deprecated; use 'names' instead. i Run `dplyr::last_dplyr_warnings()` to see the 3 remaining warnings. [ FAIL 1 | WARN 235 | SKIP 0 | PASS 153 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [179s] OK * checking PDF version of manual ... [20s] OK * checking HTML version of manual ... [6s] OK * DONE Status: 1 ERROR